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PhyDesign specifications

Information


Unique identifier OMICS_13194
Name PhyDesign
Interface Web user interface
Restrictions to use None
Input data PhyDesign reads aminoacid and DNA alignments and trees.
Input format NEXUS, FASTA, PHYLIP, NEWICK
Output data Spreadsheet outputs are offered as downloads: a compressed file containing individual rate files for each locus, and a single file containingrate site vectors for all loci. The second result provided is a graphical representation of phylogenetic informativeness and calculations of quantitative measures of informativeness. Two graphs are shown in the main section: the ultrametric tree and, aligned to it, the phylogenetic informativeness profiles.
Output format SVG
Programming languages Javascript, Perl
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Francesc López-Giráldez

Publication for PhyDesign

PhyDesign citations

 (25)
library_books

Step wise evolution of complex chemical defenses in millipedes: a phylogenomic approach

2018
Sci Rep
PMCID: 5816663
PMID: 29453332
DOI: 10.1038/s41598-018-19996-6

[…] ogous sequence sets; M2), 21% missing data (625 orthologous sequence sets; M3), and 17% missing data (312 orthologous sequence sets; M4). We also calculated data informativeness for all partitions in PhyDesign and created two datasets with an informativeness score greater than 50 (M5) and the 312 most informative partitions (M6) for 30–200 Ma, focusing on resolving the position of Stemmiulida accu […]

call_split

Aligning evidence: concerns regarding multiple sequence alignments in estimating the phylogeny of the Nudibranchia suborder Doridina

2017
R Soc Open Sci
PMCID: 5666284
PMID: 29134101
DOI: 10.1098/rsos.171095
call_split See protocol

[…] We estimated PI for each molecular marker per alignment [] through the PhyDesign web interface [], and estimated each PI profile using the site-rates model HyPhy []. First, we generated ultrametric trees by converting our concatenated Bayesian inference (BI) phylogenetic […]

call_split

A synopsis of the saddle fungi (Helvella: Ascomycota) in Europe – species delimitation, taxonomy and typification

2017
PMCID: 5832953
PMID: 29503476
DOI: 10.3767/persoonia.2017.39.09
call_split See protocol

[…] phylogenetic analyses. In order to further compare the phylogenetic informativeness (PI) of the different loci we produced a phylogenetic informativeness profile for each locus using the online tool PhyDesign (). For these analyses an ultrametric tree based on the ML tree of three loci (hsp, rpb2 and LSU) was constructed in the R package Ape (, , ). Separate analyses including more specimens from […]

call_split

Phylogenetic implications of nuclear rRNA IGS variation in Stipa L. (Poaceae)

2017
Sci Rep
PMCID: 5599551
PMID: 28912548
DOI: 10.1038/s41598-017-11804-x
call_split See protocol

[…] Phylogenetic informativeness (PI) was estimated using PhyDesign server, . PI profiles were plotted with reference to an uncalibrated tree. The tree used to overlay the historic changes in substitution rates was obtained with Maximum Likelihood method usi […]

call_split

Genomic timetree and historical biogeography of Caribbean island ameiva lizards (Pholidoscelis: Teiidae)

2017
Ecol Evol
PMCID: 5587475
PMID: 28904785
DOI: 10.1002/ece3.3157
call_split See protocol

[…] inals, so we reconstructed a chronogram for the Teiidae as follows: We used a partitioned alignment of a subset of the data (i.e., reduced number of loci, one individual per species), and implemented PhyDesign (Lopez‐Giraldez & Townsend, 2010, unpublished data) to estimate phylogenetic signal for individual loci on the topology of the MP‐EST species tree from Tucker et al. (). The 40 most informat […]

library_books

More on the Best Evolutionary Rate for Phylogenetic Analysis

2017
Syst Biol
PMCID: 5790136
PMID: 28595363
DOI: 10.1093/sysbio/syx051

[…] r Jukes–Cantor—highly uneven base frequencies would mean a reduction in effective state space) and the sequence length. A combination of bash scripts and a Perl script provided by the authors (http://phydesign.townsend.yale.edu/instructions.html) was employed to obtain an estimate for the potential excess support for the true relationship (for definitions of the terms, see ). This approach has als […]

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PhyDesign institution(s)
Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA

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